I'm still a little confused however. I read your advice in conjunction with the instructions in the FAQs for installing startup scripts and therefore put them into the /usr/local/tce.installed directory of the ISO extract filesystem. Is there any way to get them installed anywhere else on the running system? Ideally, I would like them to end up in a directory in /home/username, so I can manage the outputs a little easier.
Answering myself. I've solved this by making one startup script that copies all of the other scripts to the target area and then launches them in turn. I know it's obvious really, but I think I was thinking of the broader picture, eg a capability of copying any files to anywhere on the target system. I suspect that ezremaster doesn't do that?
Answering myself again; is that what the other blue link is for?
/usr/local/tce.installed is for extension startup scripts. Depending on what your startup scripts are doing, you probably don't need to put them in that location.
Regarding the blue links on the last page of ezremaster.. The "ISO Directory" link puts you in the location where you can make changes or add files to the ISO image. These are the files you would see when you mount the CD (i.e. the files like /boot/bzImage, /boot/isolinux/f2, etc.) Note that by default, when Tiny Core boots up the CD it was booted from is not automatically mounted.
The "initrd filesystem Directory" is what will be turned in to the tinycore.gz / initrd of your remaster. So you are free to make any changes anywhere in this filesystem that is what will become your entire root directory when the remaster boots. This allows you to customize basically any part of the system.